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- PDB-5xte: Cryo-EM structure of human respiratory complex III (cytochrome bc... -

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Entry
Database: PDB / ID: 5xte
TitleCryo-EM structure of human respiratory complex III (cytochrome bc1 complex)
Descriptorheme protein,mitochondrial
(Cytochrome ...) x 10
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Specimen sourceHomo sapiens / human
MethodElectron microscopy (3.4 Å resolution / Particle / Single particle)
AuthorsGu, J. / Wu, M. / Yang, M.
CitationCell, 2017, 170, 1247-1257.e12

Cell, 2017, 170, 1247-1257.e12 Yorodumi Papers
Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.
Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 19, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Sep 6, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 8
B: Cytochrome b-c1 complex subunit Rieske, mitochondrial
C: Cytochrome b-c1 complex subunit Rieske, mitochondrial
D: Cytochrome b-c1 complex subunit 9
E: Cytochrome b-c1 complex subunit 6, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 10
H: Cytochrome c1, heme protein, mitochondrial
J: Cytochrome b
K: Cytochrome b-c1 complex subunit 2, mitochondrial
L: Cytochrome b-c1 complex subunit 1, mitochondrial
N: Cytochrome b-c1 complex subunit 8
O: Cytochrome b-c1 complex subunit Rieske, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: Cytochrome b-c1 complex subunit 9
R: Cytochrome b-c1 complex subunit 6, mitochondrial
S: Cytochrome b-c1 complex subunit 7
T: Cytochrome b-c1 complex subunit 10
U: Cytochrome c1, heme protein, mitochondrial
V: Cytochrome b
W: Cytochrome b-c1 complex subunit 2, mitochondrial
Y: Cytochrome b-c1 complex subunit 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)497,16148
Polyers473,13422
Non-polymers24,02726
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)122840
ΔGint (kcal/M)-879
Surface area (Å2)163400

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Components

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Cytochrome ... , 11 types, 22 molecules ANBOCPDQER...

#1: Polypeptide(L)Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9791.181 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: O14949

Cellular component

Molecular function

  • ubiquinol-cytochrome-c reductase activity (GO: 0008121)

Biological process

#2: Polypeptide(L)Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 5893.814 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-57 / Source: (natural) Homo sapiens / References: UniProt: P47985, EC: 1.10.2.2

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 21645.578 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P47985, EC: 1.10.2.2

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7189.299 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: Q9UDW1

Cellular component

Molecular function

  • ubiquinol-cytochrome-c reductase activity (GO: 0008121)

Biological process

  • aerobic respiration (GO: 0009060)
  • mitochondrial electron transport, ubiquinol to cytochrome c (GO: 0006122)
  • mitochondrial respiratory chain complex III assembly (GO: 0034551)
#5: Polypeptide(L)Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 8990.854 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P07919

Cellular component

Molecular function

  • ubiquinol-cytochrome-c reductase activity (GO: 0008121)

Biological process

#6: Polypeptide(L)Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 13037.842 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-111 / Source: (natural) Homo sapiens / References: UniProt: P14927

Cellular component

Biological process

#7: Polypeptide(L)Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


Mass: 5958.912 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-52 / Source: (natural) Homo sapiens / References: UniProt: O14957

Cellular component

Molecular function

Biological process

  • generation of precursor metabolites and energy (GO: 0006091)
  • mitochondrial electron transport, ubiquinol to cytochrome c (GO: 0006122)
#8: Polypeptide(L)Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27388.395 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P08574

Cellular component

Molecular function

  • electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO: 0045155)
  • electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity (GO: 0045153)
  • heme binding (GO: 0020037)
  • metal ion binding (GO: 0046872)

Biological process

  • mitochondrial ATP synthesis coupled proton transport (GO: 0042776)
  • mitochondrial electron transport, ubiquinol to cytochrome c (GO: 0006122)
  • response to glucagon (GO: 0033762)
#9: Polypeptide(L)Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42543.016 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P00156

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 44946.582 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-453 / Source: (natural) Homo sapiens / References: UniProt: P22695

Cellular component

Molecular function

Biological process

  • aerobic respiration (GO: 0009060)
  • mitochondrial electron transport, ubiquinol to cytochrome c (GO: 0006122)
  • oxidative phosphorylation (GO: 0006119)
  • protein processing involved in protein targeting to mitochondrion (GO: 0006627)
#11: Polypeptide(L)Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 49181.430 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P31930

Cellular component

Molecular function

Biological process

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Non-polymers , 6 types, 26 molecules

#12: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / phospholipid *YM


Mass: 1464.043 Da / Num. of mol.: 9 / Formula: C81H156O17P2
#13: ChemicalChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#14: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / DOPE (phospholipid) *YM


Mass: 749.073 Da / Num. of mol.: 6 / Formula: C41H83NO8P
#15: ChemicalChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Formula: C34H34FeN4O4
#16: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4
#17: ChemicalChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 3 / Formula: C42H89NO8P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Human respiratory complex III (cytochrome bc1 complex)
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 / Source: NATURAL
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1EMAN2.1PARTICLE SELECTION1
2AutoEMation2.0IMAGE ACQUISITION1
4CTFFIND3.0CTF CORRECTION1
7COOT0.8.2MODEL FITTING1
9RELION1.4INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
11RELION1.4CLASSIFICATION1
12RELION1.4RECONSTRUCTION1
13PHENIX1.11.1MODEL REFINEMENT1
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 167761 / Symmetry type: POINT

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